Hoke left his assistant coaching position at Michigan in December 2002 to become the head football coach at his alma mater, Ball State. In six years at Ball State, Hoke was credited with turning around the football program. In 2008, he led the Ball State football team to a 12–1 record and the first appearance in the Associated Press Top 25 (peaking at No. 12) in school history. In December 2008, Hoke was hired as the head football coach at San Diego State University. He led the 2010 San Diego State Aztecs football team to the school's first nine-win season since 1971 and a victory over Navy in the 2010 Poinsettia Bowl.

He returned to Michigan after he was hired to be the program's 19th head football coach on January 11, 2011. In his inaugural season with the Wolverines he led them to an 11–2, taking Michigan to their first BCS Bowl game since the 2006 football season, where Michigan defeated the Virginia Tech Hokies in the 2012 Sugar Bowl. On December 2, 2014, Michigan fired Hoke after four seasons.

Hoke served as an assistant coach at Oregon State University from 1989 to 1994 under head coaches Dave Kragthorpe and his successor Jerry Pettibone. He was the Beavers' defensive line coach in every season except 1990, when coached the inside linebackers. The Beavers went 4–7–1 and 1–10 in Hoke's first two years in Corvallis, resulting in the firing of Kragthorpe. Hoke was retained in 1991 by Oregon State's new head coach, Jerry Pettibone. The Beavers had consecutive one-win seasons in 1991 and 1992 and back-to-back four win seasons in 1993 and 1994. Despite the team's struggles, Hoke later credited Kragthorpe with teaching him many lessons: "One of the big things coach Pettibone instilled in me was the recruiting process, and the work ethic that it takes to recruit, and the other factors, as far as trying to get a team ready every week, coming off a couple of lean years, and the intenseness of the rivalry with Oregon."[5]

In February 1995, Hoke was hired as an assistant coach at the University of Michigan under head coach Gary Moeller.[6] He was the defensive end coach in 1995 and 1996 and defensive line coach from 1997 to 2002.[7] In May 2002, Michigan head coach Lloyd Carr named Hoke as associate head coach, the only member of the staff with that distinction. At the time, Hoke told the press, "Every year you learn more and more what the head coach has to do. I'm very honored to represent this school. I grew up a big Michigan fan, and I think it's a place that's special in a lot of ways."[7] During Hoke's eight years at Michigan, the Wolverines compiled a 75–23 record, went to a bowl game every year and won the national championship in 1997. While at Michigan, Hoke was assigned to recruit in California. One of the players Hoke recruited to Michigan was Tom Brady. Hoke recalled: "Tom wasn't the greatest athlete, with those skinny legs, but there was something about him."[2]

Although Hoke was an assistant under head coaches Moeller and Carr at Michigan, Bo Schembechler remained at Michigan in the early part of Hoke's tenure. Interviewed in 2009, Hoke recalled the example set by Schembechler: "When I was at Michigan, Bo Schembechler's office was five doors down from mine. Having the opportunity to talk with him on a daily basis was something that transferred those values that are most important if you're going to be successful."[8]

Ball State

In December 2002, Hoke was hired as the 14th head football coach at his alma mater, Ball State University, signing a five-year contract at $125,000 per season.[9] He was among a group of candidates to succeed Bill Lynch, which included Illinois secondary coach Mike Mallory, Ohio State linebackers coach Mark Snyder, and Wisconsin offensive coordinator Brian White.[10] Hoke told reporters that the moment he heard the vacancy sign was out at Ball State, he knew he wanted to be the school's next head football coach: "There is no doubt."[9] Hoke added, "It is great to return to the school that enabled me to get an education and play football. I am looking forward to representing a great university with integrity and pride."[3] Michigan's head coach Lloyd Carr praised Hoke: "Brady has done a tremendous job at Michigan. He is a great recruiter. One of the things I try to do is hire people that have the potential to become head coaches. He is goal-oriented and has a great motivation to be the best that he can be."[3]

Hoke took over a Ball State football program that had not had a winning record since 1996. Hoke's teams won only 10 games in his first three seasons as head coach. Hoke began to turn this around in his fourth year as the team finished 5–7 (5–3) in 2006. In 2007, the team improved to 7–5 in the regular season, as sophomore quarterback Nate Davis passed for 3,376 yards and 27 touchdowns.[11] The 2007 Ball State team nearly upset the Nebraska Cornhuskers, but a late touchdown gave Nebraska a 41–40 win.[11] The team was invited to play in the International Bowl in Toronto, losing to Rutgers, 52–30.

During the 2008 season, Hoke led the Cardinals to the most wins in school history, finishing the regular season with an undefeated record of 12–0. The 2008 season marked the first time the Ball State Cardinals won a game against a BCS-conference opponent, a 42–20 victory over Indiana. And in October 2008, Ball State was ranked in the Associated Press Top 25 for the first time in the school's history. After his team achieved its top 25 ranking, Hoke told the media, "It's flattering obviously, but there's so much season left to play. You have to evaluate the season at the end. We've got a lot of big games ahead of us."[12] The Cardinals were ranked as high as #12 during the 2008 season.[13] After concluding an undefeated regular season, Hoke's 2008 team lost to the Buffalo Bulls in the 2008 MAC Championship Game.[12]

Ball State's rise to prominence led to Hoke's December 2008 appearance on the Late Show with David Letterman where he read a special "Top Ten List" of the "Highlights of the Ball State Cardinals Season," topped by "The Drunk 3 A.M. Coaching Tips from (Ball State alumnus) Letterman."[14]

While at Ball State, several football players were caught in a scheme to sell textbooks for classes they were not enrolled in. The NCAA cut three football scholarships and put the University on two years probation. Nine other sports were involved in the scheme.[15]

San Diego State

In December 2008, Hoke was hired as the 17th head football coach at San Diego State University. Hoke signed a five-year contract with a guaranteed payment of $3,525,000, plus incentives for hitting revenue marks and bowl berths. San Diego State was also required to pay $240,000 to buy out the remaining two years on Hoke's contract at Ball State.[16] At the press conference introducing Hoke as the Aztecs' new coach, Hoke told reporters, "Number one, this program is going to be a program that's based on toughness. To play football at the Division I level, to compete academically at the Division I level and balance both, you have to be tough-minded. You have to be physically tough and mentally tough."[16]

San Diego State compiled a 2–10 record the year before Hoke arrived. A sports writer for the San Diego Union-Tribune described the challenge facing Hoke: "It's going to be difficult for [Brady Hoke], because with the Aztecs, we're basically talking about a sea change in everything from A to Zed. This isn't Urban Meyer taking over at Florida, where the cupboard already was full of epicurean delights. State has rotting skeletons in its closet. The Aztecs haven't had a winning season since 1998, just seven since 1980."[17]

Hoke won a reputation for recruiting at San Diego State. His brother Jon Hoke, an assistant coach in the NFL, noted: "I don't care where it is, whether it's San Diego State or anywhere else, if there's one thing he can do it's recruit. He's as good at it as anybody. He's relentless with recruiting. He has a great feel for parents and a great feel for players. As long as you give him the budget to (recruit) the way it needs to be done, he'll be fine."[18]

In 2009, Hoke led the Aztecs to a record of 4–8. During the 2010 season, Hoke's team improved to 9–4. Two of the Aztecs' losses in 2010 came in close matches against ranked opponents. The Aztecs gave the undefeated, #2 TCU team its closest game of the regular season, losing by a score of 40–35. Hoke's team also lost a close game against No. 12 Missouri by a score of 27–24. The team concluded its season with a convincing 35–14 win over Navy in the 2010 Poinsettia Bowl.

Prior to the 2010 season, San Diego State had not won nine games in a season since 1971 and had not played in a bowl game since the 1998 team lost in the Las Vegas Bowl. After the 2010 season, a reporter for the Orange County Register wrote that Hoke had given San Diego State "swagger."[2]

Michigan

2011 season

On January 11, 2011, Hoke was named the 19th head football coach of the Michigan Wolverines football team.[19][20] Michigan athletic director David Brandon described some of the factors that influenced his selection of Hoke: "The reason I wanted him to be prominent in this process was simply the combination of turning around two programs, being known as a terrific recruiter, and being a defensive-minded coach with a lot of experience. Everybody that I ever talked to just raved about the quality of person he is and how much he loves Michigan."[19] Although many speculated that Hoke had been a third choice behind Jim Harbaugh and Les Miles, Brandon stated, "The job was never offered to them."[21]

On November 26, Hoke's Wolverines defeated Ohio State in Hoke's first season as the Wolverines' head coach, clinching Michigan's first 10-win season since 2006. Hoke's 2011 team also held Michigan's first winning record in Big Ten conference play since 2007. Michigan's win over Ohio State in the long-standing rivalry was its first since 2003.

Hoke won his first bowl game as the head coach of Michigan in an overtime contest against Virginia Tech by a score of 23–20. It was Michigan's first BCS bowl victory since the 2000 Orange Bowl, and its 20th bowl victory overall.[23]

2012–14 seasons

Hoke's second season in Ann Arbor started off with Michigan losing 41–14 to the defending and eventual repeat national champions, the Alabama Crimson Tide.[24] The Game was played at Cowboy Stadium on a neutral playing field, being broadcast to a nationally televised audience. Hoke said after the game "Obviously, we didn't play Michigan football, and that's something that bothers our team, bothers the coaches;" he continued "Win or lose your first game, you learn a lot."[25] Michigan ended the regular season with losses to AP #25 Nebraska (10–4), #4 Notre Dame (12–1), #3 Ohio State (12–0), and #1 Alabama (13–1),[26] before losing on the final touchdown to #8 South Carolina in the Outback Bowl, 33–28.[27]

Hoke led the 2014 Michigan team to a 5–7 record. This marked only the third season since 1975 in which Michigan missed a bowl game. The team defeated only one bowl-eligible opponent.

Following the season, Michigan fired Hoke after four seasons. Hoke compiled a 31–20 record, including an 18–14 record in Big Ten play.[28]